Writing

Some posts live on other sites I write for — marked with their domain.

• 2026-10-07 Why I Built ThinkThen
  Jev gave code a cheap, fast way to ask a question about text and get a probability back. ThinkThen wraps its three classifiers in ten plain functions, a command-line tool and 24 bindings. This post covers why I built it, what it gets wrong, and where it fits in cancer care.
• 2026-10-05 Coding Agent Proof Spirals
  Coding agents on long tasks sometimes start writing checks of their checks. This post describes that proof spiral, why workflow rules cause it, and how to stop it. The full skill is a gist you can drop into your own agent setup.
• 2026-10-05 Red, Green, Remove: Outside-In Tests for Coding Agents
  Coding agents write a small test for every step and never clean up. Cleanup skills help, but the better move is to stop making the pile. This post describes behavior first, grows tests red-green, and removes the scaffolding before landing.
• 2026-06-26 From BRAF V600E to 3D Protein Context in 3 BioMCP Commands → biomcp.org
  Three BioMCP commands take BRAF V600E from a plain variant name to residue-level protein context. The output joins UniProt, InterPro, PDB structures, AlphaFold, and Cancerhotspots.
• 2026-04-14 Daraxonrasib: Exploring a Breakthrough Cancer Drug in 6 BioMCP Commands → biomcp.org
  Revolution Medicines reported a striking survival benefit for daraxonrasib in metastatic pancreatic cancer. Six BioMCP commands trace the drug from mechanism to trials, eligibility, and safety data.
• 2026-04-09 KRAS G12C Treatment Landscape in 7 Commands → biomcp.org
  An AI agent chains 7 BioMCP commands to build a treatment picture for a KRAS G12C lung cancer patient. The run covers targeted drugs, FDA safety data, recruiting trials, and resistance mechanisms.
• 2026-03-26 Generate Charts Easily from Study Data → biomcp.org
  BioMCP compiles 12 chart types into its binary. One command renders cBioPortal study data as a PNG, an SVG, or a chart in the terminal.
• 2026-03-26 Navigate 200 Million Published Articles with BioMCP → biomcp.org
  BioMCP federates PubMed, Semantic Scholar, Europe PMC, and PubTator3 into one article command. You can search, read, triage papers, and traverse citation graphs from the terminal.
• 2026-03-26 Healthcare Agents Need Skills, Not Just Models → biomcp.org
  Curated skills lift healthcare agent pass rates from 34 percent to 86 percent on SkillBench. BioMCP ships one skill that covers more than 30 biomedical sources.
• 2026-03-24 cBioPortal Study Analytics in BioMCP → biomcp.org
  BioMCP downloads cBioPortal study datasets and runs analytics locally. The same commands produce survival analysis, co-occurrence tests, cohort comparisons, and charts.
• 2026-03-04 We Deleted 35 Tools and Our Agent Got Better → biomcp.org
  We rebuilt BioMCP from 36 MCP tools into one CLI command. The change cut context window overhead by 95 percent. The agent got faster, cheaper, and more accurate.
• 2024-01-08 What is a Custom GPT?
  Custom GPTs wrap ChatGPT with a name, instructions, knowledge files, and API actions. This post explains each configurable part and traces the product announcements that led to them. It also weighs the benefits and risks of building one.
• 2023-09-06 Using grammars to constrain llama.cpp output
  Grammars constrain llama.cpp output token by token. My biomedical extraction pipeline went from 15 to 20 percent malformed JSON to none. Extraction accuracy improved by about 25 percent.
• 2020-04-09 What is a Variant Call Format (VCF) File? → genomoncology.com
  DNA sequencing pipelines record the genetic variants they find in a VCF file. This post walks through the header, the columns, and the genotype fields.